Variant report

Variant	rs34242138
Chromosome Location	chr9:8855866-8855867
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:8855820-8855970	AoAF	blood vessel:	n/a	n/a
2	REST	chr9:8854700-8859485	H1-neurons	neurons:	n/a	chr9:8858684-8858697 chr9:8858684-8858697 chr9:8858577-8858585 chr9:8858768-8858781 chr9:8854758-8854765 chr9:8858410-8858423

Variant related genes	Relation type
ENSG00000225706	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13286924	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13292627	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2082631	0.81[AMR][1000 genomes]
rs34965880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35072441	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35884503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72704324	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72704326	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72704327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7870329	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8843000-8856600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:8845800-8856600	Weak transcription	Psoas Muscle	Psoas
3	chr9:8851200-8856400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:8853000-8856400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr9:8853200-8859000	Active TSS	Fetal Brain Female	brain
6	chr9:8853600-8858400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:8853600-8859200	Active TSS	Brain Cingulate Gyrus	brain
8	chr9:8853800-8859600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr9:8854200-8859200	Active TSS	Brain Substantia Nigra	brain
10	chr9:8854600-8856200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:8854600-8857000	Active TSS	Brain Hippocampus Middle	brain
12	chr9:8854600-8859200	Active TSS	Brain Angular Gyrus	brain
13	chr9:8854600-8859400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:8854800-8856200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:8854800-8856600	Enhancers	Liver	Liver
16	chr9:8854800-8856600	Active TSS	Brain Germinal Matrix	brain
17	chr9:8854800-8857000	Active TSS	Fetal Muscle Leg	muscle
18	chr9:8854800-8858400	Active TSS	Fetal Brain Male	brain
19	chr9:8854800-8859000	Active TSS	Brain Anterior Caudate	brain
20	chr9:8855000-8858800	Bivalent/Poised TSS	Fetal Lung	lung
21	chr9:8855000-8859000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:8855200-8857000	Active TSS	Fetal Stomach	stomach
23	chr9:8855200-8859000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:8855600-8856000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:8855600-8856000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr9:8855600-8856200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr9:8855600-8856400	Flanking Active TSS	Fetal Heart	heart
28	chr9:8855600-8857200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:8855600-8857200	Active TSS	Fetal Muscle Trunk	muscle
30	chr9:8855600-8859000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:8855600-8859000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr9:8855800-8856000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr9:8855800-8856000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
34	chr9:8855800-8856000	Flanking Active TSS	Aorta	Aorta
35	chr9:8855800-8856000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr9:8855800-8856000	Enhancers	Rectal Smooth Muscle	rectum
37	chr9:8855800-8856200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr9:8855800-8856400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr9:8855800-8856400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:8855800-8856400	Flanking Active TSS	Fetal Kidney	kidney
41	chr9:8855800-8856400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr9:8855800-8856600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
43	chr9:8855800-8856600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:8855800-8857200	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr9:8855800-8857200	Flanking Active TSS	Dnd41	blood
46	chr9:8855800-8858400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:8855800-8858800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:8855800-8858800	Active TSS	Right Atrium	heart
49	chr9:8855800-8859000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:8855800-8859000	Active TSS	Ovary	ovary

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